An artificial life approach to the origins of the genetic code

I have been invited to give a talk at the “Special workshop: The Earth, Life and Artificial Life”, sponsored by ELSI, which will take place next Friday, July 27, as part of the International Conference on Artificial Life in Tokyo.

The title and abstract are as follows:

An artificial life approach to the origins of the genetic code

Tom Froese

A growing number of artificial life researchers propose that making progress on the problem of the origins of life requires taking seriously life’s embodiment: even very simple life-like systems that are spatially individuated can interact with their environment in an adaptive manner. This behavior-based approach has also opened up new perspectives on a related unsolved problem, namely the origin of the genetic code, which can now be seen as emerging out of iterated interactions in a community of individuals. Thus, artificial life demonstrates that the dominant scientific strategy of searching for the conditions of Darwinian evolution should be broadened to consider other possibilities of optimization.

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Is there room for intrinsic normativity in a synthetic system?

I was invited to give a keynote talk at the workshop “The Synthetic Approach to Biology and the Cognitive Sciences (SA-BCS 2018): Developing an Epistemology for the Synthetic Sciences of Life and Cognition“, which will take place as part of ALIFE 2018 in Tokyo on July 25.

Here are the title and abstract of my contribution:

Is there room for intrinsic normativity in a synthetic system?

Tom Froese

Enactivism rejects the standard hypothesis of cognitive science, according to which all cognition involves the unconscious manipulation of mental representations, and instead replaces it with a dynamical systems account. And yet enactivism also resists purely dynamical approaches that see no role for any kind of subjectivity, because it appeals to the role of our lived phenomenology and claims that living beings behave with respect to intrinsic norms directed at maintaining their self-produced viability. So far, this middle way seems to be philosophically unsatisfactory: at best it allows us to claim that acting in accordance with experience or norms just is identical to a certain kind of dynamic pattern. But this turns subjectivity into a mysterious difference that makes no difference with respect to the unfolding of those patterns, which remain completely determined by the dynamical laws alone. This calls for deeper epistemological reflection about how it could be possible for subjectivity to play a role in an objective world, while avoiding a regression to the untenable positions of either representationalism or eliminativism. This debate has implications for the synthetic method, especially regarding longstanding discussions about the relative merits of software, hardware, and wetware.

The standard genetic code can evolve from a two-letter GC code

The model of an iterated learning approach the origins of the genetic code inspired this related hypothesis about a simplified precursor to the standard four-letter genetic code, which will be released in Origins of Life and Evolution of Biospheres:

The standard genetic code can evolve from a two-letter GC code without information loss or costly reassignments

Alejandro Frank and Tom Froese

It is widely agreed that the standard genetic code must have been preceded by a simpler code that encoded fewer amino acids. How this simpler code could have expanded into the standard genetic code is not well understood because most changes to the code are costly. Taking inspiration from the recently synthesized six-letter code, we propose a novel hypothesis: the initial genetic code consisted of only two letters, G and C, and then expanded the number of available codons via the introduction of an additional pair of letters, A and U. Various lines of evidence, including the relative prebiotic abundance of the earliest assigned amino acids, the balance of their hydrophobicity, and the higher GC content in genome coding regions, indicate that the original two nucleotides were indeed G and C. This process of code expansion probably started with the third base, continued with the second base, and ended up as the standard genetic code when the second pair of letters was introduced into the first base. The proposed process is consistent with the available empirical evidence, and it uniquely avoids the problem of costly code changes by positing instead that the code expanded its capacity via the creation of new codons with extra letters.

New paper on iterated learning at the origins of life

Jorge, Nathaniel and I have published an extension of our iterated learning approach to the origins of the genetic code in the Proceedings of the Artificial Life Conference 2018. We unexpectedly found that the most likely sequences in which amino acids get incorporated into the emerging genetic codes in our simulation model exhibit a remarkable overlap with the sequence predicted in the literature based on empirical considerations.

We will present this work at the ALIFE conference in Tokyo as part of the special session on “Hybrid Life: Approaches to integrate biological, artificial and cognitive systems”.

An iterated learning approach to the origins of the standard genetic code can help to explain its sequence of amino acid assignments

Tom Froese, Jorge I. Campos, and Nathaniel Virgo

Artificial life has been developing a behavior-based perspective on the origins of life, which emphasizes the adaptive potential of agent-environment interaction even at that initial stage. So far this perspective has been closely aligned to metabolism-first theories, while most researchers who study life’s origins tend to assign an essential role to RNA. An outstanding challenge is to show that a behavior-based perspective can also address open questions related to the genetic system. Accordingly, we have recently applied this perspective to one of science’s most fascinating mysteries: the origins of the standard genetic code. We modeled horizontal transfer of cellular components in a population of protocells using an iterated learning approach and found that it can account for the emergence of several key properties of the standard code. Here we further investigated the diachronic emergence of artificial codes and discovered that the model’s most frequent sequence of amino acid assignments overlaps significantly with the predictions in the literature. Our explorations of the factors that favor early incorporation into an emerging artificial code revealed two aspects: an amino acid’s relative probability of horizontal transfer, and its relative ease of discriminability in chemical space.

Figure 2

Illustration of the architecture of the genetic system of one of our hypothetical protocells.

Jorge Campos receives 2018 ISAL Award for Outstanding Student Research

I am proud to announce that the International Society for Artificial Life (ISAL) has awarded the following conference paper, which was based on Jorge’s Master’s thesis, with the “2018 ISAL Award for Outstanding Student Research”:

Campos, J.I. & Froese, T. (2017). Referential communication as a collective property of a brain-body-environment-body-brain system: A minimal cognitive model. 2017 IEEE Symposium Series on Computational Intelligence (SSCI), Honolulu, HI: IEEE Press, pp. 863-870.

Out of the nominated papers this paper was chosen as the best in terms of its scientific rigor and clarity.

The award will be announced at the ALIFE 2018 conference in Tokyo this year. alife2018-logo-screengrab

Explaining the origins of the genetic code without vertical descent

Here is the result of my two-month stay at the Earth-Life Science Institute (ELSI) of the Tokyo Institute of Technology, which was made possible by ELSI’s Origins Network. I quite like the implication that life could have been an inherently social phenomenon from its very origins!

Horizontal transfer of code fragments between protocells can explain the origins of the genetic code without vertical descent

Tom Froese, Jorge I. Campos, Kosuke Fujishima, Daisuke Kiga, and Nathaniel Virgo

Theories of the origin of the genetic code typically appeal to natural selection and/or mutation of hereditable traits to explain its regularities and error robustness, yet the present translation system presupposes high-fidelity replication. Woese’s solution to this bootstrapping problem was to assume that code optimization had played a key role in reducing the effect of errors caused by the early translation system. He further conjectured that initially evolution was dominated by horizontal exchange of cellular components among loosely organized protocells (“progenotes”), rather than by vertical transmission of genes. Here we simulated such communal evolution based on horizontal transfer of code fragments, possibly involving pairs of tRNAs and their cognate aminoacyl tRNA synthetases or a precursor tRNA ribozyme capable of catalysing its own aminoacylation, by using an iterated learning model. This is the first model to confirm Woese’s conjecture that regularity, optimality, and (near) universality could have emerged via horizontal interactions alone.

Special issue on ALIFE and society published

The organizers of 2016 edition of the International Conference on the Synthesis and Simulation of Living Systems (ALIFE VX) have edited a special issue of the journal Artificial Life by inviting extended versions of selected conference papers.

Emphasis was placed on papers related to the conference theme of “Artificial Life and Society”.

Here is a preprint of the editorial introduction:

ALife and Society: Editorial Introduction to the Artificial Life Conference 2016 Special Issue

Jesús M. Siqueiros-García, Tom Froese, Carlos Gershenson, Wendy Aguilar, Hiroki Sayama and Eduardo Izquierdo

Artificial life (ALife) research is not only about the production of knowledge, but is also a source of compelling and meaningful stories and narratives, especially now when they are needed most. Such power, so to speak, emerges from its own foundations as a discipline. It was Chris Langton in 1987 who said that “By extending the horizons of empirical research in biology beyond the territory currently circumscribed by life-as-we-know-it, the study of Artificial Life gives us access to the domain of life-as-it-could-be […]” [1]. The very notion of life-as-it-could-be opened up many possibilities to explore, and released the study of life from its material and our cognitive constraints. The study of life did not have to be limited to carbon-based entities, DNA or proteins. It could also be about general and universal processes that could be implemented and realized in multiple forms. Moreover, while ALife was about biology at the beginning, its rationale and methods are now shared by many other domains, including chemistry, engineering, and the social sciences. In other words, the power to envision and synthesize “what is possible” beyond “what is” has transcended disciplinary boundaries. It also produces the material for the exploration of narratives about how things can be in principle and not only about their current state of being.

Collective origins of the genetic code

Later today I am giving the weekly colloquium at the Center for Complexity Sciences (C3) at our main campus of UNAM. The topic will be our ongoing work on a simulation model of the collective origins of the genetic code. Details of the colloquium below:

Cartel_Coloquio C3_07-1

EON Long-Term-Visitor Award

logoI have received an EON Long-Term-Visitor Award from the director of the Earth-Life Science Institute (ELSI) of the Tokyo Institute of Technology to work for two months (June and July 2017) with Dr. Virgo and his colleagues of the ELSI Origins Network (EON).

The aim is to create an agent-based model of the origins of the genetic code based on the mechanism of horizontal gene transmission. The model is inspired by the iterated learning model of the evolution of language.

Cognitive science course next semester

Here is the information about the course I will teach at UNAM next semester.

The course will introduce ongoing debates in cognitive science about our changing understanding of the mind. Instead of being thought of as a digital computer inside the brain, mind is now widely considered to be an embodied, embedded and extended activity in the world. These ideas will be illustrated based on case studies of research in agent-based models, complex systems and human-computer interfaces, with special emphasis on demonstrating how social interactions and technologies shape our mind.

Students are not expected to program models nor to design interfaces, but to understand the implications of the new cognitive science and to apply them to their own research interests.

The course will be taught mainly in English to better prepare students for the special terms used by leading researchers in cognitive science.

For an introduction to this field, see this video: http://vimeo.com/107691239

Here is the official course information:

Posgrado en Ciencia e Ingeniería de la Computación (PCIC)

Plan: Maestría en Ciencia e Ingeniería de la Computación (Clave 80-4014)
Actividad académica: Temas Selectos de Inteligencia Artificial
Tema: Agentes autónomos y multiagentes (o: “Agentes Autónomos, Sistemas Sociales, y la Nueva Ciencia Cognitiva”)
Horarios: Lunes y Miércoles, 11:30 – 13:00
Profesor: Dr. Tom Froese

The course program can be downloaded here.

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